The long-term objective of this project is to understand the causal agents of cancer by studying functions o microRNAs (miRNAs) and their interactors such as proteins that regulate miRNA biogenesis. Recent studies link diseases such as cancer to miRNAs. MiRNAs are a class of endogenous small RNAs that negatively regulate protein production by binding to target messenger RNAs (mRNAs) with partial complementarity Although approximately 400 human miRNAs have been discovered, the functions of most are unknown. We have developed preliminary computational methods to predict miRNAs, their functions, and their interactor binding sites. Building upon our preliminary results we propose the following studies: (1) we will study the evolution of miRNAs using phylogenetic sequence analysis and predicted RNA secondary structure;(2) we will discover the functions of cancer-associated miRNAs by applying a computational method that predicts genes that are regulated by miRNAs;this objective will be achieved by development of an accurate computational algorithm that incorporates features such as mRNA structure, co-factor sequence motifs, and miRNA conservation patterns;and (3) we will identify factors that control the biogenesis of miRNAs using evolutionary genomics. The computational tools that will be developed in the proposed study will be made freely available to the scientific community. The project is timely, in light of recent realizations, which indicate that many miRNAs are aberrantly expressed in cancer, miRNAs are more useful than protein-coding genes n classifying cancers, and some miRNAs regulate large numbers (>100) of genes. We expect that the proposed study will identify new miRNAs in several species, provide new potential therapeutic targets for the treatment of cancer, and identify proteins that modulate expression of miRNAs.